CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-017731
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Lysine-specific demethylase 2B 
Protein Synonyms/Alias
 CXXC-type zinc finger protein 2; F-box and leucine-rich repeat protein 10; F-box protein FBL10; F-box/LRR-repeat protein 10; JmjC domain-containing histone demethylation protein 1B; Jumonji domain-containing EMSY-interactor methyltransferase motif protein; Protein JEMMA; Protein-containing CXXC domain 2; [Histone-H3]-lysine-36 demethylase 1B 
Gene Name
 KDM2B 
Gene Synonyms/Alias
 CXXC2; FBL10; FBXL10; JHDM1B; PCCX2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
111VPLIFREKDGLGIKMubiquitination[1]
117EKDGLGIKMPDPDFTubiquitination[1]
129DFTVRDVKLLVGSRRubiquitination[1]
147VMDVNTQKGTEMSMSubiquitination[1]
210WPQHLKEKQTEATNAubiquitination[1]
758QKMNRDNKEGQEPAKacetylation[2]
765KEGQEPAKRRSECEEacetylation[2]
890NKPLRRFKQEPEDELsumoylation[3]
1111RIDLNHCKSITPLMLubiquitination[1]
1187VQWVEGLKDAQMRDLubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [3] Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif.
 Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC.
 Mol Cell. 2010 Aug 27;39(4):641-52. [PMID: 20797634] 
Functional Description
 Histone demethylase that demethylates 'Lys-4' and 'Lys- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. 
Sequence Annotation
 DOMAIN 178 346 JmjC.
 DOMAIN 1059 1105 F-box.
 REPEAT 1093 1120 LRR 1.
 REPEAT 1133 1154 LRR 2.
 REPEAT 1156 1182 LRR 3.
 REPEAT 1222 1247 LRR 4.
 REPEAT 1248 1277 LRR 5.
 REPEAT 1278 1302 LRR 6.
 REPEAT 1303 1336 LRR 7.
 ZN_FING 606 652 CXXC-type.
 ZN_FING 659 725 PHD-type.
 METAL 242 242 Iron; catalytic (By similarity).
 METAL 244 244 Iron; catalytic (By similarity).
 METAL 314 314 Iron; catalytic (By similarity).
 BINDING 239 239 Substrate (By similarity).
 BINDING 259 259 Substrate (By similarity).
 MOD_RES 474 474 Phosphoserine.
 MOD_RES 477 477 Phosphoserine.
 MOD_RES 493 493 Phosphothreonine.
 MOD_RES 497 497 Phosphoserine.
 MOD_RES 975 975 Phosphoserine.
 MOD_RES 979 979 Phosphoserine.  
Keyword
 Alternative splicing; Chromatin regulator; Coiled coil; Complete proteome; Dioxygenase; Iron; Leucine-rich repeat; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Reference proteome; Repeat; Repressor; RNA-binding; rRNA-binding; Transcription; Transcription regulation; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1336 AA 
Protein Sequence
MAGPQMGGSA EDHPPRKRHA AEKQKKKTVI YTKCFEFESA TQRPIDRQRY DENEDLSDVE 60
EIVSVRGFSL EEKLRSQLYQ GDFVHAMEGK DFNYEYVQRE ALRVPLIFRE KDGLGIKMPD 120
PDFTVRDVKL LVGSRRLVDV MDVNTQKGTE MSMSQFVRYY ETPEAQRDKL YNVISLEFSH 180
TKLEHLVKRP TVVDLVDWVD NMWPQHLKEK QTEATNAIAE MKYPKVKKYC LMSVKGCFTD 240
FHIDFGGTSV WYHVFRGGKI FWLIPPTLHN LALYEEWVLS GKQSDIFLGD RVERCQRIEL 300
KQGYTFFIPS GWIHAVYTPV DSLVFGGNIL HSFNVPMQLR IYEIEDRTRV QPKFRYPFYY 360
EMCWYVLERY VYCVTQRSHL TQEYQRESML IDAPRKPSID GFSSDSWLEM EEEACDQQPQ 420
EEEEKDEEGE GRDRAPKPPT DGSTSPTSTP SEDQEALGKK PKAPALRFLK RTLSNESEES 480
VKSTTLAVDY PKTPTGSPAT EVSAKWTHLT EFELKGLKAL VEKLESLPEN KKCVPEGIED 540
PQALLEGVKN VLKEHADDDP SLAITGVPVV TWPKKTPKNR AVGRPKGKLG PASAVKLAAN 600
RTTAGARRRR TRCRKCEACL RTECGECHFC KDMKKFGGPG RMKQSCIMRQ CIAPVLPHTA 660
VCLVCGEAGK EDTVEEEEGK FNLMLMECSI CNEIIHPGCL KIKESEGVVN DELPNCWECP 720
KCNHAGKTGK QKRGPGFKYA SNLPGSLLKE QKMNRDNKEG QEPAKRRSEC EEAPRRRSDE 780
HSKKVPPDGL LRRKSDDVHL RKKRKYEKPQ ELSGRKRASS LQTSPGSSSH LSPRPPLGSS 840
LSPWWRSSLT YFQQQLKPGK EDKLFRKKRR SWKNAEDRMA LANKPLRRFK QEPEDELPEA 900
PPKTRESDHS RSSSPTAGPS TEGAEGPEEK KKVKMRRKRR LPNKELSREL SKELNHEIQR 960
TENSLANENQ QPIKSEPESE GEEPKRPPGI CERPHRFSKG LNGTPRELRH QLGPSLRSPP 1020
RVISRPPPSV SPPKCIQMER HVIRPPPISP PPDSLPLDDG AAHVMHREVW MAVFSYLSHQ 1080
DLCVCMRVCR TWNRWCCDKR LWTRIDLNHC KSITPLMLSG IIRRQPVSLD LSWTNISKKQ 1140
LSWLINRLPG LRDLVLSGCS WIAVSALCSS SCPLLRTLDV QWVEGLKDAQ MRDLLSPPTD 1200
NRPGQMDNRS KLRNIVELRL AGLDITDASL RLIIRHMPLL SKLHLSYCNH VTDQSINLLT 1260
AVGTTTRDSL TEINLSDCNK VTDQCLSFFK RCGNICHIDL RYCKQVTKEG CEQFIAEMSV 1320
SVQFGQVEEK LLQKLS 1336 
Gene Ontology
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; NAS:UniProtKB.
 GO:0003677; F:DNA binding; NAS:UniProtKB.
 GO:0032452; F:histone demethylase activity; TAS:BHF-UCL.
 GO:0051864; F:histone demethylase activity (H3-K36 specific); IEA:EC.
 GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:UniProtKB-KW.
 GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
 GO:0008270; F:zinc ion binding; NAS:UniProtKB.
 GO:0048596; P:embryonic camera-type eye morphogenesis; ISS:BHF-UCL.
 GO:0021592; P:fourth ventricle development; ISS:BHF-UCL.
 GO:0035518; P:histone H2A monoubiquitination; IDA:UniProtKB.
 GO:0070544; P:histone H3-K36 demethylation; IEA:GOC.
 GO:0021993; P:initiation of neural tube closure; ISS:BHF-UCL.
 GO:0021670; P:lateral ventricle development; ISS:BHF-UCL.
 GO:0030901; P:midbrain development; ISS:BHF-UCL.
 GO:0021555; P:midbrain-hindbrain boundary morphogenesis; ISS:BHF-UCL.
 GO:2000178; P:negative regulation of neural precursor cell proliferation; ISS:BHF-UCL.
 GO:0043524; P:negative regulation of neuron apoptotic process; ISS:BHF-UCL.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; ISS:BHF-UCL.
 GO:0007283; P:spermatogenesis; ISS:BHF-UCL.
 GO:0021678; P:third ventricle development; ISS:BHF-UCL.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR001810; F-box_dom_cyclin-like.
 IPR003347; JmjC_dom.
 IPR002857; Znf_CXXC.
 IPR011011; Znf_FYVE_PHD.
 IPR001965; Znf_PHD.
 IPR019787; Znf_PHD-finger. 
Pfam
 PF00646; F-box
 PF02008; zf-CXXC 
SMART
 SM00256; FBOX
 SM00558; JmjC
 SM00249; PHD 
PROSITE
 PS50181; FBOX
 PS51184; JMJC
 PS51058; ZF_CXXC
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS